Starting phenix.real_space_refine
on Thu Jul  2 11:28:59 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8d2s_27148/07_2026/8d2s_27148_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2s_27148/07_2026/8d2s_27148.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2s_27148/07_2026/8d2s_27148_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2s_27148/07_2026/8d2s_27148_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2s_27148/07_2026/8d2s_27148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2s_27148/07_2026/8d2s_27148.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1605 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      36      5.16       5
     Na      1      4.78       5
     C    4621      2.51       5
     N    1070      2.21       5
     O    1340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7071
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3577
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 475, 3523
          Classifications: {'peptide': 475}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 22, 'TRANS': 452}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 147
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 7, 'GLN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 112
      Conformer: "B"
        Number of residues, atoms: 475, 3523
          Classifications: {'peptide': 475}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 22, 'TRANS': 452}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 147
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 7, 'GLN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 112
          bond proxies already assigned to first conformer: 3555
    Chain: "B"
      Number of atoms: 1423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1423
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "C"
      Number of atoms: 1443
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 203, 1432
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
      Conformer: "B"
        Number of residues, atoms: 203, 1432
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
          bond proxies already assigned to first conformer: 1460
    Chain: "A"
      Number of atoms: 623
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 43, 587
          Ad-hoc single atom residues: {' NA': 1}
          Unusual residues: {'LMT': 17, 'ZGS': 3}
          Classifications: {'undetermined': 20, 'water': 22}
          Link IDs: {None: 40}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 147
          Unresolved non-hydrogen angles: 219
          Unresolved non-hydrogen dihedrals: 311
          Unresolved non-hydrogen chiralities: 60
      Conformer: "B"
        Number of residues, atoms: 43, 587
          Ad-hoc single atom residues: {' NA': 1}
          Unusual residues: {'LMT': 17, 'ZGS': 3}
          Classifications: {'undetermined': 20, 'water': 22}
          Link IDs: {None: 40}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 147
          Unresolved non-hydrogen angles: 219
          Unresolved non-hydrogen dihedrals: 311
          Unresolved non-hydrogen chiralities: 60
          bond proxies already assigned to first conformer: 531
    Chain: "C"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  AARG A 100 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 100 " occ=0.50
    residue:
      pdb=" N  AARG A 108 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 108 " occ=0.50
    residue:
      pdb=" N  AHIS A 420 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 420 " occ=0.50
    residue:
      pdb=" N  APHE A 427 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 427 " occ=0.50
    residue:
      pdb=" N  APHE A 449 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 449 " occ=0.50
    residue:
      pdb=" N  AARG C  13 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C  13 " occ=0.50
    residue:
      pdb=" C1 ALMT A 616 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 616 " occ=0.50
  Time building chain proxies: 1.94, per 1000 atoms: 0.27
  Number of scatterers: 7071
  At special positions: 0
  Unit cell: (73.428, 74.272, 142.636, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       3     15.00
     Na      1     11.00
     O    1340      8.00
     N    1070      7.00
     C    4621      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 130 " - pdb=" SG  CYS B 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 139 " - pdb=" SG  CYS C 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 520.2 milliseconds
  

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1604

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 11 sheets defined
      45.8% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 47
      removed outlier: 3.659A  pdb=" N   GLY A  47 " --> pdb=" O   TYR A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 68
      removed outlier: 3.829A  pdb=" N   GLN A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   GLN A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   ILE A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 100
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 109 through 128
      Proline residue:  A 118  - end of helix
      removed outlier: 3.745A  pdb=" N   TRP A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 162
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.476A  pdb=" N   SER A 167 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 200
      removed outlier: 3.555A  pdb=" N   VAL A 185 " --> pdb=" O   MET A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 213
    Processing helix  chain 'A' and resid 232 through 262
    Processing helix  chain 'A' and resid 274 through 288
    Processing helix  chain 'A' and resid 288 through 311
    Processing helix  chain 'A' and resid 312 through 319
    Processing helix  chain 'A' and resid 325 through 351
      Proline residue:  A 342  - end of helix
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 4.092A  pdb=" N   THR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 372
      removed outlier: 4.304A  pdb=" N   PHE A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   VAL A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 414
      Proline residue:  A 399  - end of helix
      Proline residue:  A 404  - end of helix
      removed outlier: 3.536A  pdb=" N   ASP A 409 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 451
      removed outlier: 4.047A  pdb=" N   GLY A 437 " --> pdb=" O   LYS A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
    Processing helix  chain 'A' and resid 473 through 488
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.703A  pdb=" N   GLN A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   ASN A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 123
    Processing helix  chain 'C' and resid 28 through 31
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5
      removed outlier: 3.777A  pdb=" N   ALA B  18 " --> pdb=" O   SER B  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.138A  pdb=" N   LYS B  11 " --> pdb=" O   ASN B 102 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   TYR B  48 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   TRP B  34 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114
      removed outlier: 4.747A  pdb=" N   ALA B 127 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ILE B 174 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   PHE B 131 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   MET B 168 " --> pdb=" O   PRO B 133 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149
      removed outlier: 4.617A  pdb=" N   TRP B 143 " --> pdb=" O   GLN B 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 58
      removed outlier: 7.031A  pdb=" N   TRP C  36 " --> pdb=" O   PRO C  47 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   ALA C  49 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL C  34 " --> pdb=" O   ALA C  49 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91
    Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.945A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA C 175 " --> pdb=" O   LEU C 159 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.945A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU C 169 " --> pdb=" O   ASN C 166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 135 through 136
    Processing sheet with id=AB2, first strand: chain 'C' and resid 149 through 151
      removed outlier: 4.743A  pdb=" N   ALA C 184 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1106 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.06

  Time building geometry restraints manager: 0.69 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.18 -     1.30: 1024
        1.30 -     1.43: 1895
        1.43 -     1.56: 4137
        1.56 -     1.68: 119
        1.68 -     1.81: 51
  Bond restraints: 7226
  Sorted by residual:
  bond pdb=" C1B LMT A 611 "
       pdb=" O5B LMT A 611 "
    ideal  model  delta    sigma   weight residual
    1.393  1.516 -0.123 2.00e-02 2.50e+03 3.76e+01
  bond pdb=" C1BBLMT A 616 "
       pdb=" O5BBLMT A 616 "
    ideal  model  delta    sigma   weight residual
    1.393  1.514 -0.121 2.00e-02 2.50e+03 3.63e+01
  bond pdb=" C1B LMT A 609 "
       pdb=" O5B LMT A 609 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.62e+01
  bond pdb=" C1B LMT A 612 "
       pdb=" O5B LMT A 612 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.57e+01
  bond pdb=" C1BALMT A 616 "
       pdb=" O5BALMT A 616 "
    ideal  model  delta    sigma   weight residual
    1.393  1.512 -0.119 2.00e-02 2.50e+03 3.54e+01
  ... (remaining 7221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.09: 9650
        6.09 -    12.18: 133
       12.18 -    18.27: 12
       18.27 -    24.36: 8
       24.36 -    30.45: 7
  Bond angle restraints: 9810
  Sorted by residual:
  angle pdb=" C06 ZGS A 601 "
        pdb=" C07 ZGS A 601 "
        pdb=" C08 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.52  157.97  -30.45 3.00e+00 1.11e-01 1.03e+02
  angle pdb=" C09 ZGS A 601 "
        pdb=" C10 ZGS A 601 "
        pdb=" C11 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.16  154.21  -27.05 3.00e+00 1.11e-01 8.13e+01
  angle pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
        pdb=" C06 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     110.70  137.41  -26.71 3.00e+00 1.11e-01 7.93e+01
  angle pdb=" C06 ZGS A 603 "
        pdb=" C07 ZGS A 603 "
        pdb=" C08 ZGS A 603 "
      ideal   model   delta    sigma   weight residual
     127.52  152.93  -25.41 3.00e+00 1.11e-01 7.17e+01
  angle pdb=" C03 ZGS A 603 "
        pdb=" C04 ZGS A 603 "
        pdb=" C05 ZGS A 603 "
      ideal   model   delta    sigma   weight residual
     127.34  152.52  -25.18 3.00e+00 1.11e-01 7.04e+01
  ... (remaining 9805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.93: 4343
       35.93 -    71.86: 230
       71.86 -   107.78: 93
      107.78 -   143.71: 33
      143.71 -   179.64: 4
  Dihedral angle restraints: 4703
    sinusoidal: 2183
      harmonic: 2520
  Sorted by residual:
  dihedral pdb=" C23 ZGS A 602 "
           pdb=" O24 ZGS A 602 "
           pdb=" P25 ZGS A 602 "
           pdb=" O26 ZGS A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.58   -2.06  179.64     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C23 ZGS A 603 "
           pdb=" O24 ZGS A 603 "
           pdb=" P25 ZGS A 603 "
           pdb=" O28 ZGS A 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
      66.18 -107.87  174.05     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C23 ZGS A 602 "
           pdb=" O24 ZGS A 602 "
           pdb=" P25 ZGS A 602 "
           pdb=" O28 ZGS A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
      66.18 -125.94 -167.88     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 4700 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 903
       0.054 -    0.109: 194
       0.109 -    0.163: 43
       0.163 -    0.217: 8
       0.217 -    0.271: 1
  Chirality restraints: 1149
  Sorted by residual:
  chirality pdb=" C1B LMT A 608 "
            pdb=" C2B LMT A 608 "
            pdb=" O1B LMT A 608 "
            pdb=" O5B LMT A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.47    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" C4' LMT A 608 "
            pdb=" C3' LMT A 608 "
            pdb=" C5' LMT A 608 "
            pdb=" O1B LMT A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.34   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" C1B LMT A 613 "
            pdb=" C2B LMT A 613 "
            pdb=" O1B LMT A 613 "
            pdb=" O5B LMT A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.41    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 1146 not shown)

  Planarity restraints: 1173
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C  46 "   -0.046 5.00e-02 4.00e+02   6.99e-02 7.82e+00
        pdb=" N   PRO C  47 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO C  47 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C  47 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 431 "    0.012 2.00e-02 2.50e+03   2.50e-02 6.25e+00
        pdb=" C   PHE A 431 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   PHE A 431 "    0.016 2.00e-02 2.50e+03
        pdb=" N   THR A 432 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  85 "    0.009 2.00e-02 2.50e+03   1.89e-02 3.58e+00
        pdb=" C   ALA A  85 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ALA A  85 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TRP A  86 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1170 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1998
        2.82 -     3.34: 6356
        3.34 -     3.86: 12101
        3.86 -     4.38: 13833
        4.38 -     4.90: 24264
  Nonbonded interactions: 58552
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 209 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG1 THR A  53 "
            pdb=" NE2 GLN A 152 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OD1 ASP A  67 "
            pdb=" OH  TYR A 452 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" NZ  LYS A 353 "
            pdb=" OD2 ASP A 405 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" O   TYR A 452 "
            pdb=" ND2 ASN C  99 "
     model   vdw
     2.353 3.120
  ... (remaining 58547 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.430
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.123   7230  Z= 0.583
  Angle     :  1.682  30.451   9818  Z= 0.619
  Chirality :  0.049   0.271   1149
  Planarity :  0.006   0.070   1173
  Dihedral  : 27.127 179.641   3087
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  5.91 %
    Favored  : 93.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.27), residues: 891
  helix:  0.58 (0.25), residues: 385
  sheet: -0.50 (0.38), residues: 189
  loop : -2.46 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  92 
 TYR   0.013   0.001   TYR A 251 
 PHE   0.016   0.002   PHE B  89 
 TRP   0.015   0.001   TRP A 140 
 HIS   0.005   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01159 /  0.58 ( 7226)
  covalent geometry    : angle       1.68301 /  0.62 ( 9810)
  SS BOND              : bond        0.00177 /  0.09 (    4)
  SS BOND              : angle       0.61595 /  0.34 (    8)
  hydrogen bonds       : bond        0.12928 /  9.07 (  383)
  hydrogen bonds       : angle       6.44581 /  4.60 ( 1106)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 140
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.8869 (m-80) cc_final: 0.8657 (m-80)
REVERT: A  132 SER cc_start: 0.8705 (p) cc_final: 0.8154 (m)
REVERT: A  134 ASP cc_start: 0.6688 (p0) cc_final: 0.6457 (p0)
REVERT: A  180 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7669 (ttp-170)
REVERT: A  345 GLN cc_start: 0.8644 (mt0) cc_final: 0.8371 (mt0)
REVERT: B   91 LYS cc_start: 0.7936 (mttt) cc_final: 0.7562 (mmtm)
REVERT: B  168 MET cc_start: 0.8467 (ttt) cc_final: 0.8262 (ttp)
REVERT: C   37 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7449 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 143
  average time/residue: 0.3441
  time to fit residues: 52.7706
Evaluate side-chains
  106 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain C residue   37 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  51 GLN
A 195 GLN
A 420 HIS    B
B 187 ASN
C  19 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.180417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.155511 restraints weight = 30741.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 3.02
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (14 function evaluations)
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7230  Z= 0.167
  Angle     :  0.800   9.799   9818  Z= 0.353
  Chirality :  0.047   0.308   1149
  Planarity :  0.005   0.063   1173
  Dihedral  : 18.396 177.998   1827
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 12.46 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.28), residues: 891
  helix:  1.36 (0.26), residues: 384
  sheet: -0.42 (0.38), residues: 195
  loop : -2.32 (0.32), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 180 
 TYR   0.011   0.001   TYR A 251 
 PHE   0.023   0.002   PHE C  38 
 TRP   0.018   0.001   TRP C  95 
 HIS   0.002   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.17 ( 7226)
  covalent geometry    : angle       0.79983 /  0.35 ( 9810)
  SS BOND              : bond        0.00244 /  0.12 (    4)
  SS BOND              : angle       0.53592 /  0.25 (    8)
  hydrogen bonds       : bond        0.04173 /  2.94 (  383)
  hydrogen bonds       : angle       4.91364 /  3.54 ( 1106)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.8853 (m-80) cc_final: 0.8611 (m-80)
REVERT: A  132 SER cc_start: 0.8740 (p) cc_final: 0.8133 (m)
REVERT: A  345 GLN cc_start: 0.8535 (mt0) cc_final: 0.8296 (mt0)
REVERT: B   91 LYS cc_start: 0.7915 (mttt) cc_final: 0.7598 (mmtm)
  outliers start: 17
  outliers final: 8
  residues processed: 116
  average time/residue: 0.3678
  time to fit residues: 45.6673
Evaluate side-chains
  112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 197 GLN
B  27 GLN
B 187 ASN
C  19 GLN
C  74 GLN
C 112 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.178197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.152358 restraints weight = 31146.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 3.01
r_work: 0.3237 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (17 function evaluations)
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7230  Z= 0.175
  Angle     :  0.697   8.609   9818  Z= 0.329
  Chirality :  0.043   0.156   1149
  Planarity :  0.005   0.069   1173
  Dihedral  : 14.881 176.816   1825
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.90 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.28), residues: 891
  helix:  1.63 (0.26), residues: 382
  sheet: -0.44 (0.39), residues: 191
  loop : -2.37 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  31 
 TYR   0.013   0.002   TYR A 179 
 PHE   0.020   0.002   PHE C  38 
 TRP   0.028   0.001   TRP C  95 
 HIS   0.004   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.17 ( 7226)
  covalent geometry    : angle       0.69749 /  0.33 ( 9810)
  SS BOND              : bond        0.00161 /  0.08 (    4)
  SS BOND              : angle       0.53020 /  0.29 (    8)
  hydrogen bonds       : bond        0.04238 /  3.00 (  383)
  hydrogen bonds       : angle       4.84750 /  3.47 ( 1106)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  106 PHE cc_start: 0.9044 (m-80) cc_final: 0.8749 (m-80)
REVERT: A  132 SER cc_start: 0.9068 (p) cc_final: 0.8608 (m)
REVERT: B   91 LYS cc_start: 0.8298 (mttt) cc_final: 0.7966 (mmtm)
REVERT: C   37 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7654 (mp)
REVERT: C  118 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7715 (mtpt)
  outliers start: 15
  outliers final: 9
  residues processed: 117
  average time/residue: 0.3801
  time to fit residues: 47.7884
Evaluate side-chains
  111 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 345 GLN
B  27 GLN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.175768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.146498 restraints weight = 34858.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 4.13
r_work: 0.3171 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (12 function evaluations)
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   7230  Z= 0.196
  Angle     :  0.692   9.358   9818  Z= 0.335
  Chirality :  0.043   0.159   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 13.958 167.033   1825
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 13.74 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.28), residues: 891
  helix:  1.60 (0.26), residues: 384
  sheet: -0.45 (0.37), residues: 203
  loop : -2.42 (0.32), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  38 
 TYR   0.015   0.002   TYR B 136 
 PHE   0.031   0.002   PHE A 431 
 TRP   0.044   0.002   TRP C  95 
 HIS   0.005   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00466 /  0.20 ( 7226)
  covalent geometry    : angle       0.69238 /  0.33 ( 9810)
  SS BOND              : bond        0.00101 /  0.05 (    4)
  SS BOND              : angle       0.64174 /  0.35 (    8)
  hydrogen bonds       : bond        0.04290 /  3.05 (  383)
  hydrogen bonds       : angle       4.86725 /  3.48 ( 1106)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  132 SER cc_start: 0.9098 (p) cc_final: 0.8614 (m)
REVERT: B   63 GLN cc_start: 0.8405 (pm20) cc_final: 0.8084 (pm20)
REVERT: B   91 LYS cc_start: 0.8463 (mttt) cc_final: 0.8077 (mmtm)
REVERT: B  105 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.6981 (tt0)
REVERT: C   37 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7792 (mp)
  outliers start: 21
  outliers final: 11
  residues processed: 106
  average time/residue: 0.3472
  time to fit residues: 39.5090
Evaluate side-chains
  106 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0050
   chunk 78 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 46 optimal weight:    8.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.5594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  63 GLN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.176820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.147204 restraints weight = 36008.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 4.39
r_work: 0.3190 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7230  Z= 0.167
  Angle     :  0.650   8.531   9818  Z= 0.315
  Chirality :  0.042   0.150   1149
  Planarity :  0.005   0.071   1173
  Dihedral  : 13.505 164.890   1825
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.38 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.28), residues: 891
  helix:  1.73 (0.26), residues: 384
  sheet: -0.35 (0.39), residues: 187
  loop : -2.37 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  38 
 TYR   0.015   0.002   TYR B 136 
 PHE   0.018   0.002   PHE B  89 
 TRP   0.036   0.002   TRP C  95 
 HIS   0.004   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.17 ( 7226)
  covalent geometry    : angle       0.65029 /  0.31 ( 9810)
  SS BOND              : bond        0.00088 /  0.05 (    4)
  SS BOND              : angle       0.56897 /  0.32 (    8)
  hydrogen bonds       : bond        0.04086 /  2.89 (  383)
  hydrogen bonds       : angle       4.72848 /  3.37 ( 1106)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  132 SER cc_start: 0.9082 (p) cc_final: 0.8612 (m)
REVERT: A  431 PHE cc_start: 0.8644 (m-80) cc_final: 0.8226 (m-80)
REVERT: B   91 LYS cc_start: 0.8412 (mttt) cc_final: 0.8000 (mmtm)
REVERT: B  105 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.6975 (tt0)
REVERT: C   37 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7752 (mt)
REVERT: C   78 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8058 (mp0)
  outliers start: 20
  outliers final: 10
  residues processed: 109
  average time/residue: 0.3634
  time to fit residues: 42.3247
Evaluate side-chains
  105 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   78 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0980
   chunk 70 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0370
   chunk 21 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0770
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.3016

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 142 GLN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.179756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.150737 restraints weight = 36759.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 3.86
r_work: 0.3243 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7230  Z= 0.128
  Angle     :  0.607   8.004   9818  Z= 0.293
  Chirality :  0.040   0.138   1149
  Planarity :  0.005   0.071   1173
  Dihedral  : 12.867 164.567   1825
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.81 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.28), residues: 891
  helix:  1.95 (0.26), residues: 385
  sheet: -0.38 (0.38), residues: 198
  loop : -2.25 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  38 
 TYR   0.012   0.001   TYR A 425 
 PHE   0.014   0.001   PHE B  89 
 TRP   0.025   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 7226)
  covalent geometry    : angle       0.60673 /  0.29 ( 9810)
  SS BOND              : bond        0.00145 /  0.07 (    4)
  SS BOND              : angle       0.42800 /  0.23 (    8)
  hydrogen bonds       : bond        0.03786 /  2.66 (  383)
  hydrogen bonds       : angle       4.54639 /  3.23 ( 1106)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  132 SER cc_start: 0.9099 (p) cc_final: 0.8616 (m)
REVERT: A  164 MET cc_start: 0.8653 (tpp) cc_final: 0.8424 (mmp)
REVERT: A  431 PHE cc_start: 0.8688 (m-80) cc_final: 0.8210 (m-80)
REVERT: B   63 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7900 (pm20)
REVERT: B   91 LYS cc_start: 0.8263 (mttt) cc_final: 0.7897 (mmtm)
REVERT: C   37 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7712 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 99
  average time/residue: 0.4054
  time to fit residues: 42.7089
Evaluate side-chains
  100 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 76 optimal weight:    0.4980
   chunk 69 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 142 GLN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.177466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.149506 restraints weight = 34248.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 3.43
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (18 function evaluations)
r_final: 0.3595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7230  Z= 0.156
  Angle     :  0.627   8.076   9818  Z= 0.304
  Chirality :  0.041   0.142   1149
  Planarity :  0.005   0.071   1173
  Dihedral  : 12.667 164.844   1825
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.13 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.28), residues: 891
  helix:  1.99 (0.26), residues: 385
  sheet: -0.34 (0.40), residues: 182
  loop : -2.26 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  38 
 TYR   0.014   0.002   TYR A 425 
 PHE   0.019   0.002   PHE B  89 
 TRP   0.035   0.001   TRP C  95 
 HIS   0.004   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.16 ( 7226)
  covalent geometry    : angle       0.62709 /  0.30 ( 9810)
  SS BOND              : bond        0.00102 /  0.05 (    4)
  SS BOND              : angle       0.50122 /  0.27 (    8)
  hydrogen bonds       : bond        0.03951 /  2.80 (  383)
  hydrogen bonds       : angle       4.57638 /  3.25 ( 1106)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  132 SER cc_start: 0.8717 (p) cc_final: 0.8123 (m)
REVERT: A  180 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7781 (ttt90)
REVERT: A  431 PHE cc_start: 0.8495 (m-80) cc_final: 0.8196 (m-80)
REVERT: B   91 LYS cc_start: 0.7997 (mttt) cc_final: 0.7703 (mmtm)
REVERT: C   37 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7417 (mp)
REVERT: C   78 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7675 (mt-10)
  outliers start: 16
  outliers final: 10
  residues processed: 102
  average time/residue: 0.3583
  time to fit residues: 39.1826
Evaluate side-chains
  102 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   78 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0970
   chunk 70 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0060
   chunk 85 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0970
   overall best weight:    0.3192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  63 GLN
B 142 GLN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.180215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.155396 restraints weight = 28338.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.76
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3695 r_free = 0.3695    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3695 r_free = 0.3695    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7230  Z= 0.127
  Angle     :  0.588   7.519   9818  Z= 0.285
  Chirality :  0.040   0.140   1149
  Planarity :  0.005   0.071   1173
  Dihedral  : 12.054 165.207   1825
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.97 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.29), residues: 891
  helix:  2.11 (0.26), residues: 385
  sheet: -0.32 (0.38), residues: 198
  loop : -2.21 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  38 
 TYR   0.014   0.001   TYR A 425 
 PHE   0.015   0.001   PHE B  89 
 TRP   0.024   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 7226)
  covalent geometry    : angle       0.58786 /  0.29 ( 9810)
  SS BOND              : bond        0.00127 /  0.06 (    4)
  SS BOND              : angle       0.47416 /  0.25 (    8)
  hydrogen bonds       : bond        0.03699 /  2.60 (  383)
  hydrogen bonds       : angle       4.43333 /  3.15 ( 1106)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  132 SER cc_start: 0.8691 (p) cc_final: 0.8078 (m)
REVERT: A  180 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7791 (ttt90)
REVERT: A  184 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8070 (mt-10)
REVERT: A  431 PHE cc_start: 0.8304 (m-80) cc_final: 0.8043 (m-80)
REVERT: B   91 LYS cc_start: 0.7814 (mttt) cc_final: 0.7609 (mmtm)
REVERT: C   19 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7896 (tp40)
REVERT: C   37 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7380 (mp)
REVERT: C   78 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7133 (mt-10)
  outliers start: 17
  outliers final: 10
  residues processed: 106
  average time/residue: 0.4028
  time to fit residues: 45.3462
Evaluate side-chains
  107 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   19 GLN
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   78 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 71 optimal weight:    0.0070
   chunk 36 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0470
   chunk 53 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0980
   chunk 85 optimal weight:    0.6980
   chunk 9 optimal weight:    0.1980
   chunk 32 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   overall best weight:    0.1696

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 142 GLN
B 187 ASN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.182123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.154186 restraints weight = 35012.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 3.52
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7230  Z= 0.111
  Angle     :  0.574   7.724   9818  Z= 0.279
  Chirality :  0.039   0.139   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 11.645 165.743   1825
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.77 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.29), residues: 891
  helix:  2.24 (0.26), residues: 383
  sheet: -0.26 (0.38), residues: 199
  loop : -2.19 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  38 
 TYR   0.015   0.001   TYR A 425 
 PHE   0.013   0.001   PHE B  89 
 TRP   0.018   0.001   TRP C  95 
 HIS   0.001   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 7226)
  covalent geometry    : angle       0.57438 /  0.28 ( 9810)
  SS BOND              : bond        0.00234 /  0.11 (    4)
  SS BOND              : angle       0.47453 /  0.25 (    8)
  hydrogen bonds       : bond        0.03563 /  2.49 (  383)
  hydrogen bonds       : angle       4.36176 /  3.10 ( 1106)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  132 SER cc_start: 0.8661 (p) cc_final: 0.8053 (m)
REVERT: A  180 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7745 (ttt90)
REVERT: A  184 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7926 (mt-10)
REVERT: A  431 PHE cc_start: 0.8447 (m-80) cc_final: 0.8185 (m-80)
REVERT: B   91 LYS cc_start: 0.7818 (mttt) cc_final: 0.7604 (mmtm)
REVERT: B  168 MET cc_start: 0.8597 (ttt) cc_final: 0.8379 (ttp)
REVERT: C   37 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7362 (mp)
  outliers start: 14
  outliers final: 9
  residues processed: 104
  average time/residue: 0.4165
  time to fit residues: 46.0875
Evaluate side-chains
  106 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0670
   chunk 68 optimal weight:    0.0870
   chunk 64 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0000
   overall best weight:    0.2700

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 142 GLN
B 187 ASN
C  19 GLN
C  74 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.180570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.155385 restraints weight = 33146.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 3.03
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7230  Z= 0.120
  Angle     :  0.578   7.702   9818  Z= 0.282
  Chirality :  0.040   0.136   1149
  Planarity :  0.005   0.070   1173
  Dihedral  : 11.211 166.387   1825
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.77 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.29), residues: 891
  helix:  2.26 (0.26), residues: 383
  sheet: -0.17 (0.39), residues: 199
  loop : -2.16 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  38 
 TYR   0.015   0.001   TYR B 136 
 PHE   0.016   0.001   PHE B  89 
 TRP   0.023   0.001   TRP C  95 
 HIS   0.002   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 7226)
  covalent geometry    : angle       0.57842 /  0.28 ( 9810)
  SS BOND              : bond        0.00216 /  0.11 (    4)
  SS BOND              : angle       0.43682 /  0.22 (    8)
  hydrogen bonds       : bond        0.03584 /  2.52 (  383)
  hydrogen bonds       : angle       4.33932 /  3.08 ( 1106)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  132 SER cc_start: 0.8694 (p) cc_final: 0.8098 (m)
REVERT: A  180 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7758 (ttt90)
REVERT: A  184 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7944 (mt-10)
REVERT: A  431 PHE cc_start: 0.8436 (m-80) cc_final: 0.8187 (m-80)
REVERT: B   91 LYS cc_start: 0.7844 (mttt) cc_final: 0.7629 (mmtm)
REVERT: B  168 MET cc_start: 0.8617 (ttt) cc_final: 0.8410 (ttp)
REVERT: C   19 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.6872 (tp-100)
REVERT: C   37 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7274 (mp)
  outliers start: 12
  outliers final: 9
  residues processed: 97
  average time/residue: 0.4723
  time to fit residues: 48.9797
Evaluate side-chains
  101 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   19 GLN
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  174 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 187 ASN
C  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.180614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.155411 restraints weight = 26204.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.78
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.229   7230  Z= 0.254
  Angle     :  0.997  59.187   9818  Z= 0.572
  Chirality :  0.054   1.230   1149
  Planarity :  0.005   0.071   1173
  Dihedral  : 11.217 166.395   1825
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.93 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.29), residues: 891
  helix:  2.26 (0.26), residues: 383
  sheet: -0.19 (0.39), residues: 199
  loop : -2.16 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  38 
 TYR   0.015   0.001   TYR B 136 
 PHE   0.016   0.001   PHE B  89 
 TRP   0.022   0.001   TRP C  95 
 HIS   0.002   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00477 /  0.25 ( 7226)
  covalent geometry    : angle       0.99766 /  0.57 ( 9810)
  SS BOND              : bond        0.00193 /  0.09 (    4)
  SS BOND              : angle       0.44726 /  0.23 (    8)
  hydrogen bonds       : bond        0.03596 /  2.53 (  383)
  hydrogen bonds       : angle       4.34779 /  3.08 ( 1106)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1839.58 seconds
wall clock time: 32 minutes 14.29 seconds (1934.29 seconds total)